update: fix the first two steps
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parent
1227280755
commit
50f99a9575
1 changed files with 45 additions and 5 deletions
50
RGBEPP.d
50
RGBEPP.d
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@ -175,15 +175,51 @@ void processQcTrim(string[] ARG_L, int ARG_T, string DirRaw, string DirQcTrim, s
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writeln("QcTrimming::End");
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}
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void processMappingDenovo(string[] ARG_L, int ARG_T, string DirQcTrim, string DirAssembly, string DirMap, string PathBowtie2, string PathSamtools){
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void processAssemMv(string[] ARG_L,string DirAssembly){
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// Prepare
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string DirAssemblySca = DirAssembly ~ "/" ~ "scaffolds";
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string DirAssemblyCont = DirAssembly ~ "/" ~ "contigs";
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writeln("Assembly_Move::Start");
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createDir(DirAssemblySca);
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createDir(DirAssemblyCont);
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foreach (string file; ARG_L ){
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string baseName = getBaseName(file);
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string DirAssemblyInd = DirAssembly ~ "/" ~ baseName;
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string inputSca = DirAssemblyInd ~ "/" ~ "scaffolds.fasta";
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string inputCont = DirAssemblyInd ~ "/" ~ "contigs.fasta";
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string outputSca = DirAssemblySca ~ "/" ~ baseName ~ ".fasta";
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string outputCont = DirAssemblyCont ~ "/" ~ baseName ~ ".fasta";
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if (!exists(inputSca)) {
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writeln("File not found: ", inputSca);
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continue;
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} else {
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copy(inputSca, outputSca);
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}
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if (!exists(inputCont)) {
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writeln("File not found: ", inputCont);
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continue;
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} else {
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copy(inputCont, outputCont);
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}
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}
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writeln("Assembly_Move::End");
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}
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void processMappingDenovo(string[] ARG_L, string ARG_R, int ARG_T, string DirQcTrim, string DirAssembly, string DirMap, string PathBowtie2, string PathSamtools){
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// Prepare directory
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writeln("Mapping::Start");
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createDir(DirMap);
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createDir(DirMap ~ "/index");
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string DirAssemblySca = DirAssembly ~ "/" ~ "scaffolds";
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string DirAssemblyFas = DirAssembly ~ "/" ~ "fasta";
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createDir(DirAssemblySca);
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createDir(DirAssemblyFas);
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string ReferDmnd = DirAssemblySca ~ "/" ~ "Reference.dmnd";
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string ARG_R_Base = getBaseName(ARG_R);
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string ARG_R_Ref = DirAssemblyFas ~ "/" ~ ARG_R_Base ~ ".fasta";
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copy(ARG_R, ARG_R_Ref);
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string [] cmdDmMakeDB = [ "diamond", "makedb", "--db", "Reference", "--in", ARG_R_Ref];
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executeCommand(cmdDmMakeDB);
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string ReferDmnd = DirAssemblyFas ~ "/" ~ "Reference.dmnd";
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string PathBowtie2_build = PathBowtie2 ~ "-build";
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foreach (string file; ARG_L) {
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@ -207,6 +243,7 @@ void processMappingDenovo(string[] ARG_L, int ARG_T, string DirQcTrim, string Di
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executeCommandPipe([cmdMap, cmdSam2Bam]);
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}
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writeln("Mapping::End");
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}
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void processMapping(string[] ARG_L, string ARG_R, int ARG_T, string DirQcTrim, string DirMap, string PathBowtie2, string PathSamtools) {
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@ -628,16 +665,18 @@ void main(string[] args) {
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}
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}
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if (ARG_F == "assembly") {
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if (ARG_F == "all" || ARG_F == "assembly") {
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if(testFiles([PathSpades])){
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processAssembly(ARG_L, ARG_M, ARG_T, DirQcTrim, DirAssembly, PathSpades);
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processAssemMv(ARG_L, DirAssembly);
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}
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}
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if (ARG_F == "all" || ARG_F == "map") {
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if(testFiles([PathBowtie2, PathSamtools])){
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//processMapping(ARG_L, ARG_R, ARG_T, DirQcTrim, DirMap, PathBowtie2, PathSamtools);
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processMappingDenovo(ARG_L, ARG_T, DirQcTrim, DirAssembly, DirMap, PathBowtie2, PathSamtools);
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processMappingDenovo(ARG_L, ARG_R, ARG_T, DirQcTrim, DirAssembly, DirMap, PathBowtie2, PathSamtools);
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}
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}
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@ -653,6 +692,7 @@ void main(string[] args) {
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processVarCallDenovo(ARG_L, ARG_T, DirAssembly, DirMap, DirBam, DirVcf, PathBcftools);
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}
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}
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if (ARG_F == "all" || ARG_F == "consen") {
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